Ok sorry. I did that, but the output of splice junctions is empty. The other outputs looks fine. What might be the problem?
> Shall I replace:Yes, that's correct.
>
> /orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19
>
> with
>
> hg19 hg19 hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
Finally, please email only galaxy-dev with questions about local installations; galaxy-user is for questions about how to use Galaxy.
Best,
J.